added check for qcli
updated to import command line processing functionality from qcli
added qcli to dependency list
updated changelog to mention qcli dependency
removed as we're now using code from qcli
removed make_qiime_rst_file.py in favor of qcli_make_rst
updated changelog
ported run_script_usage_tests to qcli
ported qiime_system_call to qcli
updated to reflect new parameter names since prot to qcli
ported timeout functionality to qcli
Merge pull request #1006 from gregcaporaso/qcli-port

modifications to qiime to use command line interface framework from qcli

Note, this works fine but not sure about: 
                         qcli version:	0.0.0-dev
Update tutorial.rst
Merge pull request #1011 from casaburi/master

Update tutorial.rst
Removed file extension check for .fan and .qual files with split_libraries.py as this caused issues with galaxy
Fixed order bug for unit test issue #988
Merge pull request #1016 from walterst/test_pick_otus_order_bug

Fixed order bug for unit test issue #988
Merge pull request #1015 from walterst/split_libraries_file_check

Removed file extension check for .fan and .qual files with split_librari...
fixes #1017

more extensive testing to follow - this is a commit of the first working version
modifications to documentation and output filenames